DOCSLIB.ORG

Downloaded from Dbgap

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

bioRxiv preprint doi: https://doi.org/10.1101/507939; this version posted December 28, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Sex-specific regulatory mechanisms underlying Hepatocellular 2 Carcinoma 3 4 Heini M Natri1,*, Melissa Wilson Sayres1, Kenneth Buetow1 5 6 1 Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, 7 Arizona, USA 8 9 Corresponding author: 10 E-mail: [email protected] (H.M.N) 1 bioRxiv preprint doi: https://doi.org/10.1101/507939; this version posted December 28, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 11 Abstract 12 Sex differences in cancer occurrence and mortality are evident across tumor types; men exhibit 13 higher rates of incidence and often poorer responses to treatment. Targeted approaches to the 14 treatment of tumors that account for these sex differences require the characterization and 15 understanding of the fundamental biological mechanisms that differentiate them. Hepatocellular 16 Carcinoma (HCC) is the second leading cause of cancer death worldwide, with the incidence 17 rapidly rising. HCC exhibits a male-bias in occurrence and mortality. Most HCC studies, to date, 18 have failed to explore the sex-specific effects in gene regulatory functions. Here we have 19 characterized the regulatory functions underlying HCC tumors in sex-stratified and combined 20 analyses. By sex-specific analyses of differential expression of tumor and tumor adjacent 21 samples, we uncovered etiologically relevant genes, pathways and canonical networks 22 differentiating male and female HCC. While both sexes exhibited activation of pathways related 23 to apoptosis and p53 signaling, pathways involved in innate and adaptive immunity showed 24 differential activation between the sexes. Using eQTL analyses, we discovered germline 25 regulatory variants with differential effects on tumor gene expression between the sexes. We 26 discovered eQTLs overlapping HCC GWAS loci, providing regulatory mechanisms connecting 27 these loci to HCC risk. Furthermore, we discovered genes under germline regulatory control that 28 alter survival in patients with HCC, including some that exhibited differential effects on survival 29 between the sexes. Overall, our results provide new insight into the role of genetic regulation of 30 transcription in modulating sex differences in HCC occurrence and outcome and provide a 31 framework for future studies on sex-biased cancers. 32 Author Summary 33 Sex differences in cancer occurrence and mortality are evident across tumor types, and targeted 34 approaches to the treatment male and female tumors require the characterization and 2 bioRxiv preprint doi: https://doi.org/10.1101/507939; this version posted December 28, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 35 understanding of the fundamental biological mechanisms that differentiate them. Hepatocellular 36 Carcinoma (HCC) is the second leading cause of cancer death worldwide, with the incidence 37 rapidly rising. HCC exhibits a male-bias in occurrence and mortality. Here, we have characterized 38 the regulatory functions underlying male and female HCC. We show that while HCC shares 39 commonalities across the sexes, it shows demonstrable regulatory differences that could be 40 critical in terms of prevention and treatment: we detected differential activation of pathways 41 involved in innate and adaptive immunity, as well as differential genetic effects on gene 42 expression, between the sexes. Furthermore, we have detected regulatory variants overlapping 43 known HCC GWAS risk loci, providing regulatory mechanisms connecting these risk variants to 44 HCC. Finally, we discovered genes under germline regulatory control altering the overall survival 45 of patients with HCC, including some that showed differential effects between the sexes. Overall, 46 our findings create a paradigm for future studies on sex-biased cancers. 47 Introduction 48 Differences in cancer occurrence and mortality between sexes are evident across tumor types; 49 males exhibit higher rates of cancer incidence and often poorer response to treatment, including 50 some forms of chemotherapy and immunotherapy [1,2]. While differences in risk behaviors and 51 environmental exposure may explain some portion of the sex-bias, cellular and molecular 52 differences are also likely to be important. The sexes differ in their endocrinological profile, 53 immunological functions and genetic makeup [3–5]. However, sex differences are rarely 54 considered in the development of cancer therapies, and the contribution from sex chromosome 55 variation to tumor etiology remains poorly understood. Sex-biased gene expression and 56 regulatory functions may underlie differences between the sexes in disease prevalence and 57 severity [6,7]. Analyses of sex-specific regulation of gene expression are essential for 3 bioRxiv preprint doi: https://doi.org/10.1101/507939; this version posted December 28, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 58 understanding sources of sex difference in cancer incidence, as well as sex-specific mechanisms 59 affecting tumor etiology, disease progression and outcome. 60 Hepatocellular carcinoma (HCC) exhibits sex-bias in occurrence, with a male-to-female 61 incidence ratio between 1.3:1 and 5.5:1 across populations [8,9]. HCC is the second leading cause 62 of cancer mortality worldwide, accounting for 8.2% of all cancer deaths [10]. HCC risk is 63 influenced by genetic susceptibility, environmental factors such as oncogenic viral infections, 64 metabolic syndrome, and alcohol use, and shaped by numerous biological processes, resulting in 65 a high degree of genetic and transcriptional heterogeneity [11]. HCC incidence in the US has 66 doubled in the last 3 decades, attributable to increased rates of obesity [9]. 67 While sex-bias in HCC is partly attributed to sex-specific differences in risk behaviors and 68 environmental exposure, the relationship of these factors and sex as a biological variable has not 69 been systematically investigated. Previously, sex differences in HCC were explored in 70 conjunction with 12 additional Cancer Genome Atlas (TCGA) tumor types by Yuan et al [12]. 71 They discovered extensive sex-biased signatures in gene expression in HCC and other strongly 72 sex-biased cancers. 73 HCC shows evidence of molecular subtypes, though their role in sex-bias has yet to be explored. 74 More specifically, clustering analyses of gene expression data have produced a characterization 75 of four distinct HCC subtypes that differ in terms of gene expression, pathway enrichment, and 76 median survival [13]. A study utilizing a weighted co-expression network analysis method 77 discovered hub genes associated with HCC outcome [14]. On the other hand, genetic variants 78 affecting the expression of TNFRSF10 [15], PAX8 [16], and PVT1 [17] have been found to alter 79 HCC disease progression and outcome, highlighting the role of regulatory variants in HCC. How 80 these progression altering subtypes or variants are related to HCC sex-bias has not been 81 examined. 4 bioRxiv preprint doi: https://doi.org/10.1101/507939; this version posted December 28, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 82 Sex-specific analyses can reveal genetic and regulatory mechanisms of sexual dimorphism in 83 HCC susceptibility, progression, and mortality. Targeted approaches to the treatment of male and 84 female HCC will require the characterization and understanding of the fundamental biological 85 mechanisms that differentiate them. Here, we analyzed data from The Genotype-Tissue 86 Expression (GTEx) project and The Cancer Genome Atlas (TCGA) to examine the sex-specific 87 patterns of gene expression and regulation in HCC and healthy liver tissue. We find etiologically 88 meaningful differences in regulatory functions in HCC between males and females, providing 89 insight into the mechanisms underlying sex-bias in cancer. Additionally, we observed genes 90 under germline regulatory control that alter survival in sex-biased way in patients with HCC. 91 Results 92 Sex-specific patterns of gene expression HCC 93 We found sex-differences in gene expression in normal liver, tumor adjacent, and tumor tissues 94 (Fig 1). We found 13 genes showing a consistent sex-bias in expression in liver, HCC adjacent 95 tissue and HCC. Notably, we find that X-inactivation and X-linked dosage compensation appear 96 to be functioning in the healthy liver, HCC adjacent and HCC tissues. This is concluded from the 97 bulk RNAseq measurements where we observe XIST expression
Recommended publications
  • Autism Multiplex Family with 16P11.2P12.2 Microduplication Syndrome in Monozygotic Twins and Distal 16P11.2 Deletion in Their Brother

    Autism Multiplex Family with 16P11.2P12.2 Microduplication Syndrome in Monozygotic Twins and Distal 16P11.2 Deletion in Their Brother

    European Journal of Human Genetics (2012) 20, 540–546 & 2012 Macmillan Publishers Limited All rights reserved 1018-4813/12 www.nature.com/ejhg ARTICLE Autism multiplex family with 16p11.2p12.2 microduplication syndrome in monozygotic twins and distal 16p11.2 deletion in their brother Anne-Claude Tabet1,2,3,4, Marion Pilorge2,3,4, Richard Delorme5,6,Fre´de´rique Amsellem5,6, Jean-Marc Pinard7, Marion Leboyer6,8,9, Alain Verloes10, Brigitte Benzacken1,11,12 and Catalina Betancur*,2,3,4 The pericentromeric region of chromosome 16p is rich in segmental duplications that predispose to rearrangements through non-allelic homologous recombination. Several recurrent copy number variations have been described recently in chromosome 16p. 16p11.2 rearrangements (29.5–30.1 Mb) are associated with autism, intellectual disability (ID) and other neurodevelopmental disorders. Another recognizable but less common microdeletion syndrome in 16p11.2p12.2 (21.4 to 28.5–30.1 Mb) has been described in six individuals with ID, whereas apparently reciprocal duplications, studied by standard cytogenetic and fluorescence in situ hybridization techniques, have been reported in three patients with autism spectrum disorders. Here, we report a multiplex family with three boys affected with autism, including two monozygotic twins carrying a de novo 16p11.2p12.2 duplication of 8.95 Mb (21.28–30.23 Mb) characterized by single-nucleotide polymorphism array, encompassing both the 16p11.2 and 16p11.2p12.2 regions. The twins exhibited autism, severe ID, and dysmorphic features, including a triangular face, deep-set eyes, large and prominent nasal bridge, and tall, slender build. The eldest brother presented with autism, mild ID, early-onset obesity and normal craniofacial features, and carried a smaller, overlapping 16p11.2 microdeletion of 847 kb (28.40–29.25 Mb), inherited from his apparently healthy father.
  • Mutation Analysis of Genes Within the Dynactin Complex in a Cohort of Hereditary Peripheral Neuropathies

    Mutation Analysis of Genes Within the Dynactin Complex in a Cohort of Hereditary Peripheral Neuropathies

    Clin Genet 2016: 90: 127–133 © 2015 John Wiley & Sons A/S. Printed in Singapore. All rights reserved Published by John Wiley & Sons Ltd CLINICAL GENETICS doi: 10.1111/cge.12712 Original Article Mutation analysis of genes within the dynactin complex in a cohort of hereditary peripheral neuropathies a a Tey S., Ahmad-Annuar A., Drew A.P., Shahrizaila N., Nicholson G.A., S. Tey , A. Ahmad-Annuar , Kennerson M.L. Mutation analysis of genes within the dynactin complex in A.P. Drewb, N. Shahrizailac, , a cohort of hereditary peripheral neuropathies. G.A. Nicholsonb d and Clin Genet 2016: 90: 127–133. © John Wiley & Sons A/S. Published by M.L. Kennersonb,d John Wiley & Sons Ltd, 2015 aDepartment of Biomedical Science, The cytoplasmic dynein–dynactin genes are attractive candidates for Faculty of Medicine, University of Malaya, b neurodegenerative disorders given their functional role in retrograde Kuala Lumpur, Malaysia, Northcott transport along neurons. The cytoplasmic dynein heavy chain (DYNC1H1) Neuroscience Laboratory, ANZAC Research Institute, and Sydney Medical gene has been implicated in various neurodegenerative disorders, and School, University of Sydney, Sydney, dynactin 1 (DCTN1) genes have been implicated in a wide spectrum of Australia, cDepartment of Medicine, disorders including motor neuron disease, Parkinson’s disease, spinobulbar Faculty of Medicine, University of Malaya, muscular atrophy and hereditary spastic paraplegia. However, the Kuala Lumpur, Malaysia, and dMolecular involvement of other dynactin genes with inherited peripheral neuropathies Medicine Laboratory, Concord Hospital, (IPN) namely, hereditary sensory neuropathy, hereditary motor neuropathy Sydney, Australia and Charcot–Marie–Tooth disease is under reported. We screened eight genes; DCTN1-6 and ACTR1A and ACTR1B in 136 IPN patients using Key words: Charcot–Marie–Tooth – whole-exome sequencing and high-resolution melt (HRM) analysis.
  • (New Ref)-CG-MS

    (New Ref)-CG-MS

    Send Orders for Reprints to [email protected] 522 Current Genomics, 2018, 19, 522-602 REVIEW ARTICLE Early Life Stress and Epigenetics in Late-onset Alzheimer’s Dementia: A Systematic Review Erwin Lemche* Section of Cognitive Neuropsychiatry, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK Abstract: Involvement of life stress in Late-Onset Alzheimer’s Disease (LOAD) has been evinced in longitudinal cohort epidemiological studies, and endocrinologic evidence suggests involvements of catecholamine and corticosteroid systems in LOAD. Early Life Stress (ELS) rodent models have suc- cessfully demonstrated sequelae of maternal separation resulting in LOAD-analogous pathology, thereby supporting a role of insulin receptor signalling pertaining to GSK-3beta facilitated tau hyper- phosphorylation and amyloidogenic processing. Discussed are relevant ELS studies, and findings from three mitogen-activated protein kinase pathways (JNK/SAPK pathway, ERK pathway, p38/MAPK pathway) relevant for mediating environmental stresses. Further considered were the roles of auto- phagy impairment, neuroinflammation, and brain insulin resistance. For the meta-analytic evaluation, 224 candidate gene loci were extracted from reviews of animal stud- ies of LOAD pathophysiological mechanisms, of which 60 had no positive results in human LOAD association studies. These loci were combined with 89 gene loci confirmed as LOAD risk genes in A R T I C L E H I S T O R Y previous GWAS and WES. Of the 313 risk gene loci evaluated, there were 35 human reports on epi- Received: July 01, 2017 genomic modifications in terms of methylation or histone acetylation. 64 microRNA gene regulation Revised: July 27, 2017 mechanisms were published for the compiled loci.
  • Supplementary Information – Postema Et Al., the Genetics of Situs Inversus Totalis Without Primary Ciliary Dyskinesia

    Supplementary Information – Postema Et Al., the Genetics of Situs Inversus Totalis Without Primary Ciliary Dyskinesia

    1 Supplementary information – Postema et al., The genetics of situs inversus totalis without primary ciliary dyskinesia Table of Contents: Supplementary Methods 2 Supplementary Results 5 Supplementary References 6 Supplementary Tables and Figures Table S1. Subject characteristics 9 Table S2. Inbreeding coefficients per subject 10 Figure S1. Multidimensional scaling to capture overall genomic diversity 11 among the 30 study samples Table S3. Significantly enriched gene-sets under a recessive mutation model 12 Table S4. Broader list of candidate genes, and the sources that led to their 13 inclusion Table S5. Potential recessive and X-linked mutations in the unsolved cases 15 Table S6. Potential mutations in the unsolved cases, dominant model 22 2 1.0 Supplementary Methods 1.1 Participants Fifteen people with radiologically documented SIT, including nine without PCD and six with Kartagener syndrome, and 15 healthy controls matched for age, sex, education and handedness, were recruited from Ghent University Hospital and Middelheim Hospital Antwerp. Details about the recruitment and selection procedure have been described elsewhere (1). Briefly, among the 15 people with radiologically documented SIT, those who had symptoms reminiscent of PCD, or who were formally diagnosed with PCD according to their medical record, were categorized as having Kartagener syndrome. Those who had no reported symptoms or formal diagnosis of PCD were assigned to the non-PCD SIT group. Handedness was assessed using the Edinburgh Handedness Inventory (EHI) (2). Tables 1 and S1 give overviews of the participants and their characteristics. Note that one non-PCD SIT subject reported being forced to switch from left- to right-handedness in childhood, in which case five out of nine of the non-PCD SIT cases are naturally left-handed (Table 1, Table S1).
  • Wo 2010/065567 A2

    Wo 2010/065567 A2

    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date 10 June 2010 (10.06.2010) WO 2010/065567 A2 (51) International Patent Classification: (81) Designated States (unless otherwise indicated, for every A61K 36/889 (2006.01) A61K 31/16 (2006.01) kind of national protection available): AE, AG, AL, AM, A61K 36/736 (2006.01) A61K 31/05 (2006.01) AO, AT, AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ, A61K 31/166 (2006.01) A61P 5/00 (2006.01) CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, (21) International Application Number: HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, PCT/US2009/066294 KR, KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, (22) International Filing Date: ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, 1 December 2009 (01 .12.2009) NO, NZ, OM, PE, PG, PH, PL, PT, RO, RS, RU, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TJ, TM, TN, TR, TT, (25) Filing Language: English TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (26) Publication Language: English (84) Designated States (unless otherwise indicated, for every (30) Priority Data: kind of regional protection available): ARIPO (BW, GH, 61/1 18,945 1 December 2008 (01 .12.2008) US GM, KE, LS, MW, MZ, NA, SD, SL, SZ, TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, MD, RU, TJ, (71) Applicant (for all designated States except US): LIFES¬ TM), European (AT, BE, BG, CH, CY, CZ, DE, DK, EE, PAN EXTENSION LLC [US/US]; 933 First Colonial ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, Road, Suite 114, Virginia Beach, VA 23454 (US).
  • Identification and Functional Characterisation of Oncogenic Pathway Signatures in Malignant Lymphoma

    Identification and Functional Characterisation of Oncogenic Pathway Signatures in Malignant Lymphoma

    Identification and functional characterisation of oncogenic pathway signatures in malignant Lymphoma Doctoral Thesis In partial fulfilment of the requirements for the degree “Doctor rerum naturalium (Dr. rer. nat.)” in the Molecular Medicine Study Program at the Georg-August University Göttingen Graduate School 1034 submitted by Alexandra Schrader born in Soest Göttingen, 2011 Thesis Committee Prof Dr. Dieter Kube (Supervisor) E-Mail [email protected] Phone 0049-551-391537 Postal Address Universitätsmedizin Göttingen Zentrum Innere Medizin Abteilung Hämatologie und Onkologie Robert-Koch-Straße 40 37075 Göttingen Prof Dr. Heidi Hahn E-Mail [email protected] Phone 0049-551-39-14010 Postal Address Universitätsmedizin Göttingen Zentrum Hygiene und Humangenetik Institut für Humangenetik Heinrich-Düker-Weg 12 37073 Göttingen Prof Dr. Martin Oppermann E-Mail [email protected] Phone 0049-551-395822 Postal Address Universitätsmedizin Göttingen Zentrum Hygiene und Humangenetik Abteilung Zelluläre und Molekulare Immunologie Humboldtallee 34 37073 Göttingen Date of Disputation: 22.09.2011 Affidavit By this I declare that I independently authored the presented thesis: “Identification and functional characterisation of oncogenic pathway signatures in malignant Lymphoma” and that I did not use other auxiliary means than indicated. Paragraphs that are taken from other publications, by wording or by sense, are marked in every case with a specification of the literary source. Furthermore I declare that I carried out the scientific experiments following
  • Association of Common PALB2 Polymorphisms with Breast Cancer Risk

    Association of Common PALB2 Polymorphisms with Breast Cancer Risk

    Cancer Prevention and Susceptibility Association of Common PALB2 Polymorphisms with Breast Cancer Risk: A Case-Control Study Peizhan Chen,1Jie Liang,2 Zhanwei Wang,2 Xiaoyi Zhou,2 Lu Chen,1Mian Li,1Dong Xie,1 Zhibin Hu,2 Hongbing Shen,2 and Hui Wang1 Abstract Purpose: The PALB2 gene has an essential role in BRCA2-mediated DNA double-strand break repair and intra ^ S phase DNA damage checkpoint control, and its mutations are moderately associated with breast cancer susceptibility.This study was designed to investigate the common variants of PALB2 and theirassociation with breast cancerrisk. Experimental Design: Foursingle nucleotide polymorphisms (SNP; rs249954, rs249935, rs120963, and rs16940342) which tagged all 19 of the reported SNPs (minor allele frequency >0.05) covering PALB2 were selected and genotyped in 1,049 patients with breast cancer and 1,073 cancer-free controls in a female Chinese population. Results: Based on the multiple hypothesis testing with the Benjamini-Hochberg method, tagging SNPs (tSNP) rs249954, rs120963, and rs16940342 were found to be associated with an increase of breast cancer risk (false discovery rate ^ adjusted P values of 0.004, 0.028, and 0.049, respectively) under the dominant model. tSNP rs249954 was associated with a 36% increase of breast cancer risk [adjusted odds ratio (OR), 1.36; 95% confidence intervals (CI), 1.13 -1. 6 4; P = 0.001;TT/TC versus CC genotypes]. The adjusted OR for rs120963 was 1.25 (95% CI, 1.04-1.49; P = 0.014; CC/CT versusTTgenotypes). For rs16940342, the adjusted OR was1.21 (95% CI,1.02-1.45; P = 0.037; GG/GA versus AA genotypes).
  • In a Single Wei Inset Patent Application Publication Aug

    In a Single Wei Inset Patent Application Publication Aug

    US 20150217131A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2015/0217131 A1 Titova et al. (43) Pub. Date: Aug. 6, 2015 (54) TERAHERTZ PULSE RADATION IN Publication Classification TREATING SKINDSORDERS (51) Int. Cl. (71) Applicants: The Governors of the University of A6IN5/06 (2006.01) Alberta, Edmonton (CA); The (52) U.S. Cl. University of Lethbridge, Lethbridge CPC ......... A61N5/0616 (2013.01); A61N 2005/066 (CA) (2013.01) (72) Inventors: Lyubov Titova, Edmonton (CA); Frank Hegmann, Edmonton (CA); Olga (57) ABSTRACT Kovalchuk, Lethbridge, (CA) (21) Appl. No.: 14/615,153 The disclosure provides methods for the treatment of skin disorders through the use of minimally invasive terahertz (22) Filed: Feb. 5, 2015 radiation. The method includes exposing skin cells to tera hertz radiation in amount Sufficient to modulate gene expres Related U.S. Application Data sion in the skin cells. The modulation of gene expression then (60) Provisional application No. 61/936,627, filed on Feb. results in a reduction of the disease state or aspects thereof in 6, 2014. the exposed skin cells. S.. R S S. & S. S. S. S. & S. S. S.s S ŠS. S.S. ^x S.S. & S.N SS. S.S S S. S S S S R S. Ski SS 8 in a single wei inset Patent Application Publication Aug. 6, 2015 Sheet 1 of 60 US 2015/0217131 A1 º?%-?.- & & cy Figure 1A Figure 1B Figure 1C Patent Application Publication Aug. 6, 2015 Sheet 2 of 60 US 2015/0217131 A1 Staturn E. S as Figure 1D S S.
  • HHS Public Access Author Manuscript

    HHS Public Access Author Manuscript

    HHS Public Access Author manuscript Author Manuscript Author ManuscriptNature. Author ManuscriptAuthor manuscript; Author Manuscript available in PMC 2015 November 28. Published in final edited form as: Nature. 2015 May 28; 521(7553): 520–524. doi:10.1038/nature14269. Global genetic analysis in mice unveils central role for cilia in congenital heart disease You Li1,8, Nikolai T. Klena1,8, George C Gabriel1,8, Xiaoqin Liu1,7, Andrew J. Kim1, Kristi Lemke1, Yu Chen1, Bishwanath Chatterjee1, William Devine2, Rama Rao Damerla1, Chien- fu Chang1, Hisato Yagi1, Jovenal T. San Agustin5, Mohamed Thahir3,4, Shane Anderton1, Caroline Lawhead1, Anita Vescovi1, Herbert Pratt5, Judy Morgan6, Leslie Haynes6, Cynthia L. Smith6, Janan T. Eppig6, Laura Reinholdt6, Richard Francis1, Linda Leatherbury7, Madhavi K. Ganapathiraju3,4, Kimimasa Tobita1, Gregory J. Pazour5, and Cecilia W. Lo1,9 1Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 2Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 3Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA 4Intelligent Systems Program, School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA 9Corresponding author. [email protected] Phone: 412-692-9901, Mailing address: Dept of Developmental Biology, Rangos Research Center, 530 45th St, Pittsburgh, PA, 15201. 8Co-first authors Author Contributions: Study design: CWL ENU mutagenesis, line cryopreservation, JAX strain datasheet construction:
  • Qt49s0g99h.Pdf

    Qt49s0g99h.Pdf

    Copyright 2012 By Ernest Tsz-Tsun Lam ! ii Acknowledgements This dissertation represents a body of work that many have contributed to, and there are countless people that I must thank. I offer my most sincere gratitude to those that have helped in one way or another and those that have lent their support in making this possible. First and foremost, I would like to thank Prof. Pui-Yan Kwok for being my mentor and graduate advisor. He took me in when I knew little about genetics (let alone genomics) and research in general. He has entrusted me with the optical mapping project that he has been so passionate about, and for that, I am extremely grateful. He is always supportive. He has given me the freedom and time I needed to grow and develop as an independent scientist. Most importantly, he has created an environment that fosters collaboration instead of competition. He has brought in so many genuinely nice people to this lab, and this has had an unquantifiable positive impact on my graduate work. I am grateful to past and present members of the Kwok Lab; it is an honor to have worked with all of you. In this age of Big Science, one could not conceal the fact that most of our work requires extensive collaboration. Our lab members are our most immediate collaborators. Angel Mak – thank you for your honesty and thoughtfulness. You have helped me see and appreciate things with your childlike sense of wonder. You should believe in yourself, that you truly are special in your own ways.
  • Child and Adolescent Psychiatric Genetics Johannes Hebebrand, Andre Scherag, Benno G

    Child and Adolescent Psychiatric Genetics Johannes Hebebrand, Andre Scherag, Benno G

    Child and adolescent psychiatric genetics Johannes Hebebrand, Andre Scherag, Benno G. Schimmelmann, Anke Hinney To cite this version: Johannes Hebebrand, Andre Scherag, Benno G. Schimmelmann, Anke Hinney. Child and adolescent psychiatric genetics. European Child and Adolescent Psychiatry, Springer Verlag (Germany), 2010, 19 (3), pp.259-279. 10.1007/s00787-010-0091-y. hal-00563486 HAL Id: hal-00563486 https://hal.archives-ouvertes.fr/hal-00563486 Submitted on 6 Feb 2011 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Eur Child Adolesc Psychiatry (2010) 19:259–279 DOI 10.1007/s00787-010-0091-y REVIEW Child and adolescent psychiatric genetics Johannes Hebebrand • Andre Scherag • Benno G. Schimmelmann • Anke Hinney Received: 14 December 2009 / Accepted: 8 January 2010 / Published online: 6 February 2010 Ó Springer-Verlag 2010 Abstract The current status of child and adolescent the introductory article of this special issue of the European psychiatric genetics appears promising in light of the ini- Child and Adolescent Psychiatry. tiation of genome-wide association studies (GWAS) for diverse polygenic disorders and the molecular elucidation Keywords Candidate gene Á Linkage Á Rett syndrome Á of monogenic Rett syndrome, for which recent functional Gene–environment interaction Á Genome-wide studies provide hope for pharmacological treatment strat- association study egies.
  • Molecular Sciences High-Resolution Chromosome Ideogram Representation of Currently Recognized Genes for Autism Spectrum Disorder

    Molecular Sciences High-Resolution Chromosome Ideogram Representation of Currently Recognized Genes for Autism Spectrum Disorder

    Int. J. Mol. Sci. 2015, 16, 6464-6495; doi:10.3390/ijms16036464 OPEN ACCESS International Journal of Molecular Sciences ISSN 1422-0067 www.mdpi.com/journal/ijms Article High-Resolution Chromosome Ideogram Representation of Currently Recognized Genes for Autism Spectrum Disorders Merlin G. Butler *, Syed K. Rafi † and Ann M. Manzardo † Departments of Psychiatry & Behavioral Sciences and Pediatrics, University of Kansas Medical Center, Kansas City, KS 66160, USA; E-Mails: [email protected] (S.K.R.); [email protected] (A.M.M.) † These authors contributed to this work equally. * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +1-913-588-1873; Fax: +1-913-588-1305. Academic Editor: William Chi-shing Cho Received: 23 January 2015 / Accepted: 16 March 2015 / Published: 20 March 2015 Abstract: Recently, autism-related research has focused on the identification of various genes and disturbed pathways causing the genetically heterogeneous group of autism spectrum disorders (ASD). The list of autism-related genes has significantly increased due to better awareness with advances in genetic technology and expanding searchable genomic databases. We compiled a master list of known and clinically relevant autism spectrum disorder genes identified with supporting evidence from peer-reviewed medical literature sources by searching key words related to autism and genetics and from authoritative autism-related public access websites, such as the Simons Foundation Autism Research Institute autism genomic database dedicated to gene discovery and characterization. Our list consists of 792 genes arranged in alphabetical order in tabular form with gene symbols placed on high-resolution human chromosome ideograms, thereby enabling clinical and laboratory geneticists and genetic counsellors to access convenient visual images of the location and distribution of ASD genes.